20180725-2-Gastroc-002-powder_S2 vs 20180725-3-Gastroc-002-powder_S3

ATAC-seq on motrpac

Report generated at 2018-10-27 03:55:57

Pipeline type: ATAC-Seq

Peak caller: MACS2

Flagstat QC (raw BAM)

	rep1	rep2
Total	43339412	65787412
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	43062943	64369053
Mapped(QC-failed)	0	0
% Mapped	99.3600	97.8400
Paired	24584078	32781498
Paired(QC-failed)	0	0
Read1	12292039	16390749
Read1(QC-failed)	0	0
Read2	12292039	16390749
Read2(QC-failed)	0	0
Properly Paired	24066130	31075436
Properly Paired(QC-failed)	0	0
% Properly Paired	97.8900	94.8000
With itself	24260918	31308026
With itself(QC-failed)	0	0
Singletons	46691	55113
Singletons(QC-failed)	0	0
% Singleton	0.1900	0.1700
Diff. Chroms	52333	59446
Diff. Chroms (QC-failed)	0	0

Flagstat QC (filtered BAM)

	rep1	rep2
Total	16972830	18904942
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	16972830	18904942
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	16972830	18904942
Paired(QC-failed)	0	0
Read1	8486415	9452471
Read1(QC-failed)	0	0
Read2	8486415	9452471
Read2(QC-failed)	0	0
Properly Paired	16972830	18904942
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	16972830	18904942
With itself(QC-failed)	0	0
Singletons	0	0
Singletons(QC-failed)	0	0
% Singleton	0.0000	0.0000
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

MarkDuplicate QC

	rep1	rep2
Unpaired Reads	0	0
Paired Reads	9395807	10681883
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	909392	1229412
Paired Opt. Dupes	4567	4432
% Dupes/100	0.0968	0.1151

Library complexity QC

	rep1	rep2
Total Read Pairs	9171371	10562098
Distinct Read Pairs	8323666	9372160
One Read Pair	7544689	8295254
Two Read Pairs	715743	974306
NRF = Distinct/Total	0.9076	0.8873
PBC1 = OnePair/Distinct	0.9064	0.8851
PBC2 = OnePair/TwoPair	10.5411	8.5140

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Enrichment (strand cross-correlation measures) QC

	rep1	rep2
Reads	8311019	9357705
Est. Fragment Len.	0	0
Corr. Est. Fragment Len.	0.1949	0.1503
Phantom Peak	70	60
Corr. Phantom Peak	0.1581	0.1295
Argmin. Corr.	1500	1500
Min. Corr.	0.1128	0.1218
NSC	1.7272	1.2340
RSC	1.8135	3.7017

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Enrichment QC (Fraction of reads in MACS2 raw peaks)

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	ppr1	ppr2
Fraction of Reads in Peak	0.2670	0.1432	0.2931	0.1753	0.2922	0.1742	0.1896	0.2034	0.2025

repX: MACS2 peaks from true replicate X
repX-prY: MACS2 peaks from Yth pseudoreplicates from replicate X
pooled: MACS2 peaks from pooled true replicates
ppr1: MACS2 peaks from 1st pooled pseudo replicates
ppr2: MACS2 peaks from 2nd pooled pseudo replicates

Reproducibility QC and Peak Detection Statistics

	overlap	IDR
Nt	87204	26262
N1	93092	41952
N2	38760	14980
Np	107775	47189
N optimal	107775	47189
N conservative	87204	26262
Optimal Set	ppr	ppr
Conservative Set	rep1-rep2	rep1-rep2
Rescue Ratio	1.2359	1.7969
Self Consistency Ratio	2.4018	2.8005
reproducibility	borderline	borderline

Overlapping peaks

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

IDR (Irreproducible Discovery Rate) peaks

N1: Replicate 1 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consistent IDR 0.05 peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Enrichment QC (Fraction of reads in overlapping peaks)

	rep1-rep2	rep1-pr	rep2-pr	ppr
Fraction of Reads in Peak	0.1147	0.1890	0.0445	0.1302

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Enrichment QC (Fraction of reads in IDR peaks)

	rep1-rep2	rep1-pr	rep2-pr	ppr
Fraction of Reads in Peak	0.0605	0.1277	0.0260	0.0855

ppr: IDR peaks comparing pooled pseudo replicates
rep1-pr: IDR peaks comparing pseudoreplicates from replicate 1
rep2-pr: IDR peaks comparing pseudoreplicates from replicate 2
repi-repj: IDR peaks comparing true replicates (rep i vs. rep j)

IDR (Irreproducible Discovery Rate) plots